rs2159128

Positions:

• chr19-950380-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005224.3(ARID3A):​c.694-9712G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.022 (187 hom., cov: 0)
• Consequence: ARID3A NM_005224.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.758

Genes affected

ARID3A (HGNC:3031): (AT-rich interaction domain 3A) This gene encodes a member of the ARID (AT-rich interaction domain) family of DNA binding proteins. It was found by homology to the Drosophila dead ringer gene, which is important for normal embryogenesis. Other ARID family members have roles in embryonic patterning, cell lineage gene regulation, cell cycle control, transcriptional regulation, and possibly in chromatin structure modification. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.118 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARID3A	NM_005224.3	c.694-9712G>T		intron_variant		ENST00000263620.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARID3A	ENST00000263620.8	c.694-9712G>T		intron_variant		1	NM_005224.3	P1
ARID3A	ENST00000587532.5	c.235-9712G>T		intron_variant		5
ARID3A	ENST00000457152.3	c.179-9712G>T		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0224 AC: 859 AN: 38396 Hom.: 185 Cov.: 0

Gnomad AFR AF: 0.0284

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0596

Gnomad ASJ AF: 0.00192

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.0391

Gnomad FIN AF: 0.0304

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00288

Gnomad OTH AF: 0.0174

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0225 AC: 864 AN: 38426 Hom.: 187 Cov.: 0 AF XY: 0.0239 AC XY: 464 AN XY: 19374

Gnomad4 AFR AF: 0.0290

Gnomad4 AMR AF: 0.0601

Gnomad4 ASJ AF: 0.00192

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.0394

Gnomad4 FIN AF: 0.0304

Gnomad4 NFE AF: 0.00288

Gnomad4 OTH AF: 0.0170

Alfa AF: 0.0528 Hom.: 23

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.8
DANN	Benign	0.58

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2159128; hg19: chr19-950380;